############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scRepertoire_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck’ * using R version 4.5.0 Patched (2025-04-21 r88169) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scRepertoire/DESCRIPTION’ ... OK * this is package ‘scRepertoire’ version ‘2.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scRepertoire’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'StartracDiversity.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'alluvialClones.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalAbundance.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalBias.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalDiversity.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalHomeostasis.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalLength.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalNetwork.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalOccupy.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalOverlap.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalProportion.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalQuant.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalRarefaction.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalScatter.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalSizeDistribution.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentAA.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentGenes.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentKmer.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentVJ.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'positionalEntropy.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'positionalProperty.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'vizGenes.Rd': ‘[grDevices:palettes]{hcl.pals}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clonalSizeDistribution 33.986 3.628 38.015 StartracDiversity 6.850 0.334 7.244 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: • percentAA/percentaa-plot.svg • percentGenes/percentgenes-order-plot.svg • percentKmer/percentkmer-group-motif2-order-plot.svg • percentVJ/percentvj-order-plot.svg • positionalEntropy/positionalentropy-tra-plot.svg • positionalEntropy/positionalentropy-trb-order-plot.svg • positionalProperty/positionalentropy-kidera-plot.svg • positionalProperty/positionalentropy-stscales-plot.svg • positionalProperty/positionalentropy-tra-plot.svg • positionalProperty/positionalentropy-trb-order-plot.svg • positionalProperty/positionalentropy-tscales-plot.svg • positionalProperty/positionalentropy-vhse-plot.svg • vizGenes/vizgenes-heatmap-vignette-plot.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’ for details.